ZCCHC12

zinc finger CCHC-type containing 12, the group of Paraneoplastic Ma antigens|Zinc fingers CCHC-type

Basic information

Region (hg38): X:118823824-118826968

Links

ENSG00000174460 ∙ NCBI:170261 ∙ OMIM:300701 ∙ HGNC:27273 ∙ Uniprot:Q6PEW1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZCCHC12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC12 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	2

Variants in ZCCHC12

This is a list of pathogenic ClinVar variants found in the ZCCHC12 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-118825263-C-T			Benign (Jul 05, 2018)
X-118825341-C-A		not specified	Conflicting classifications of pathogenicity (Dec 01, 2022)
X-118825344-G-A		not specified	Conflicting classifications of pathogenicity (Oct 09, 2024)
X-118825350-A-G			Uncertain significance (Aug 01, 2023)
X-118825352-A-G		not specified	Uncertain significance (Oct 01, 2024)
X-118825364-G-A		not specified	Uncertain significance (Sep 10, 2024)
X-118825368-G-A		not specified	Uncertain significance (Feb 23, 2023)
X-118825537-T-C		not specified	Uncertain significance (Aug 20, 2024)
X-118825677-G-C		not specified	Uncertain significance (Dec 14, 2023)
X-118825688-T-C			Likely benign (Mar 01, 2023)
X-118825695-C-G		not specified	Uncertain significance (Sep 30, 2021)
X-118825702-A-G		not specified	Uncertain significance (Apr 23, 2024)
X-118825705-T-A		not specified	Uncertain significance (Mar 29, 2023)
X-118825737-A-G		not specified	Uncertain significance (Jul 19, 2023)
X-118825857-C-T			Likely benign (Jun 01, 2022)
X-118825885-G-T		not specified	Uncertain significance (Feb 21, 2025)
X-118825938-C-A		not specified	Uncertain significance (Feb 14, 2023)
X-118825967-G-T		not specified	Uncertain significance (Dec 31, 2024)
X-118826029-A-G		not specified	Uncertain significance (Apr 14, 2022)
X-118826081-G-A		ZCCHC12-related disorder	Benign (Jun 11, 2019)
X-118826106-C-T		not specified	Likely benign (Dec 21, 2024)
X-118826116-G-T		not specified	Uncertain significance (Mar 08, 2024)
X-118826187-A-T		not specified	Uncertain significance (Sep 04, 2024)
X-118826212-G-A		not specified	Uncertain significance (Jul 08, 2022)
X-118826215-G-T		not specified	Uncertain significance (Aug 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC12	protein_coding	protein_coding	ENST00000310164	1	3179

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0465	0.863	125733	1	6	125740	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.683	138	162	0.849	0.0000125	2656
Missense in Polyphen		24	32.535	0.73766		678
Synonymous	-0.587	70	64.0	1.09	0.00000494	812
Loss of Function	1.39	3	6.97	0.431	5.98e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000244	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000157	0.0000980
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional coactivator in the bone morphogenetic protein (BMP)-signaling pathway. It positively modulates BMP signaling by interacting with SMAD1 and associating with CBP in the transcription complex. It contributes to the BMP-induced enhancement of cholinergic-neuron-specific gene expression (By similarity). {ECO:0000250}.
• Pathway: Regulation of nuclear beta catenin signaling and target gene transcription (Consensus)

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• loftool: 0.356
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.227
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.694

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Zcchc12

Gene ontology

• Biological process: BMP signaling pathway;positive regulation of nucleic acid-templated transcription
• Cellular component: nuclear speck
• Molecular function: nucleic acid binding;protein binding;zinc ion binding;nuclear receptor transcription coactivator activity